1M70 | pdb_00001m70

Crystal structure of oxidized recombinant cytochrome c4 from Pseudomonas stutzeri

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1ETP	PDB entry 1ETP

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.6	298	0.2M ammonium acetate, 0.1M sodium citrate pH 5.6, 30%(w/v) PEG 4000, pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
1.76	30.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 74.96	α = 90
b = 57.64	β = 104.23
c = 84.41	γ = 90

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	120	IMAGE PLATE	MARRESEARCH	Osmic mirrors	2000-12-07	M	SINGLE WAVELENGTH
2	1	x-ray	100	IMAGE PLATE	MARRESEARCH	Mirror	2001-01-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU300	1.54179
2	SYNCHROTRON	MAX II BEAMLINE I711	1.03260	MAX II	I711

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1,2	1.25	30	90.9			178812	175219

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1,2	1.25	1.29	77

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 1ETP	1.25	30	171606	152386	8596	88.8	0.1571	0.1571	0.1547	0.16	0.2021	0.17	RANDOM

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]

Coordinate Error
Structure Solution Method	Refinement High Resolution	Refinement Low Resolution
10	5368	6688

RMS Deviations
Key	Refinement Restraint Deviation
s_similar_dist	0.453
s_approx_iso_adps	0.077
s_non_zero_chiral_vol	0.07
s_zero_chiral_vol	0.063
s_similar_adp_cmpnt	0.048
s_angle_d	0.028
s_anti_bump_dis_restr	0.028
s_from_restr_planes	0.0268
s_bond_d	0.011
s_rigid_bond_adp_cmpnt	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5512
Nucleic Acid Atoms
Solvent Atoms	819
Heterogen Atoms	350

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
SHELXL-97	refinement

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.